Immobiliser reactivate?

I have a Ford 1986 Ford Fiesta/Soho. Mazda endura motor. I recently removed the battery to fix the clutch mechanism and when I put everything back it would not start I put inthe radio coding and it works fine and system has an anti hijack system with and immobiliser in the key as a transponder mechanism. the anti-hijack system flashes and when deactivated it also works or deactivate the only problem is the factory fitted key with transponder internal does not activate to cause the vehicle to start. Pleeeeeease can someone help I am technically literate and if told the sequence I am confident that I would fix the problem as appossed to paying Ford unnecessary monies.